Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent
Despite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other targets...
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MDPI AG
2025-06-01
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| Online Access: | https://www.mdpi.com/2218-273X/15/6/805 |
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| author | Prasanna V. Shekar Anuj Kumar Nirmitee Mulgaonkar Samneet Kashyap Gourav Choudhir Sandun Fernando Sachin Rustgi |
| author_facet | Prasanna V. Shekar Anuj Kumar Nirmitee Mulgaonkar Samneet Kashyap Gourav Choudhir Sandun Fernando Sachin Rustgi |
| author_sort | Prasanna V. Shekar |
| collection | DOAJ |
| description | Despite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other targets as well. The spike protein is crucial for the virus’s entry into host cells. The aptamer development process for the spike protein’s receptor binding domain (RBD) begins with splitting the SARS-CoV-2’s genome into 40 nucleotide-long sequences, predicting their two-dimensional structure, and sorting based on the free energy. Selected oligomers undergo three-dimensional structure prediction and docking onto the viral spike protein’s RBD. Six RNA oligomers were identified as top candidates based on the RNA docking with the SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1 strain) and Omicron variant BA.1 RBD and molecular dynamics simulations. Three oligomers also demonstrated strong predicted binding affinity with other SARS-CoV-2 variants, including BA.2, XBB.1.5, and EG.5, based on the protein–aptamer docking followed by stability evaluation using the MD simulations. The aptamer with the best fit for the spike protein RBD was later validated using biolayer interferometry. The process has resulted in identifying a single aptamer from a library of 29,000 RNA oligomers, which exhibited affinity in the submicromolar range and the potential to develop into a viral screen or therapeutic. |
| format | Article |
| id | doaj-art-c501bdc8a21142598acf78c637ef7b08 |
| institution | Kabale University |
| issn | 2218-273X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj-art-c501bdc8a21142598acf78c637ef7b082025-08-20T03:26:21ZengMDPI AGBiomolecules2218-273X2025-06-0115680510.3390/biom15060805Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic AgentPrasanna V. Shekar0Anuj Kumar1Nirmitee Mulgaonkar2Samneet Kashyap3Gourav Choudhir4Sandun Fernando5Sachin Rustgi6Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USADepartment of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, CanadaBiological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USADepartment of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USACentre for Rural Development & Technology, Indian Institute of Technology (IIT), New Delhi 110016, IndiaBiological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USADepartment of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USADespite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other targets as well. The spike protein is crucial for the virus’s entry into host cells. The aptamer development process for the spike protein’s receptor binding domain (RBD) begins with splitting the SARS-CoV-2’s genome into 40 nucleotide-long sequences, predicting their two-dimensional structure, and sorting based on the free energy. Selected oligomers undergo three-dimensional structure prediction and docking onto the viral spike protein’s RBD. Six RNA oligomers were identified as top candidates based on the RNA docking with the SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1 strain) and Omicron variant BA.1 RBD and molecular dynamics simulations. Three oligomers also demonstrated strong predicted binding affinity with other SARS-CoV-2 variants, including BA.2, XBB.1.5, and EG.5, based on the protein–aptamer docking followed by stability evaluation using the MD simulations. The aptamer with the best fit for the spike protein RBD was later validated using biolayer interferometry. The process has resulted in identifying a single aptamer from a library of 29,000 RNA oligomers, which exhibited affinity in the submicromolar range and the potential to develop into a viral screen or therapeutic.https://www.mdpi.com/2218-273X/15/6/805<i>in silico</i> SELEX (systematic evolution of ligands by exponential enrichment)aptamerSARS-CoV-2COVID-19 |
| spellingShingle | Prasanna V. Shekar Anuj Kumar Nirmitee Mulgaonkar Samneet Kashyap Gourav Choudhir Sandun Fernando Sachin Rustgi Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent Biomolecules <i>in silico</i> SELEX (systematic evolution of ligands by exponential enrichment) aptamer SARS-CoV-2 COVID-19 |
| title | Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent |
| title_full | Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent |
| title_fullStr | Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent |
| title_full_unstemmed | Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent |
| title_short | Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent |
| title_sort | aptamer development for sars cov 2 and omicron variants using the spike protein receptor binding domain as a potential diagnostic tool and therapeutic agent |
| topic | <i>in silico</i> SELEX (systematic evolution of ligands by exponential enrichment) aptamer SARS-CoV-2 COVID-19 |
| url | https://www.mdpi.com/2218-273X/15/6/805 |
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